def insertion(xgr1, xgr2):
""" find an insertion transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
idxs = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
if len(xgrs1) == 2 and len(xgrs2) == 1:
xgra, xgrb = xgrs1
atmsa = atoms(xgra)
atmsb = atoms(xgrb)
neighsa = atom_neighbor_keys(xgra)
neighsb = atom_neighbor_keys(xgrb)
bndsa = bond_keys(xgra)
bndsb = bond_keys(xgrb)
tra = _insertion(atmsa, neighsa, bndsa, atmsb, neighsb, xgr1, xgr2)
idxs = [0, 1]
if not tra:
tra = _insertion(atmsb, neighsb, bndsb, atmsa, neighsa, xgr1, xgr2)
if tra:
idxs = [1, 0]
else:
idxs = None
elif len(xgrs1) == 1 and len(xgrs2) == 1:
xgra = xgr1
idxs = [0]
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
bndsa = bond_keys(xgra)
tra = _insertion(atmsa, neighsa, bndsa, atmsa, neighsa, xgr1, xgr2)
return tra, idxs
def substitution(xgr1, xgr2):
"""identifies substitution reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
idxs = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
print('len xgrs test:', len(xgrs1), len(xgrs2))
print('xgrs test:', xgrs1, xgrs2)
if len(xgrs1) == 2 and len(xgrs2) == 2:
xgra, xgrb = xgrs1
xgrc, xgrd = xgrs2
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
bndsa = bond_keys(xgra)
atmsb = atoms(xgrb)
neighsb = atom_neighbor_keys(xgrb)
bndsb = bond_keys(xgrb)
atmsc = atoms(xgrc)
neighsc = atom_neighbor_keys(xgrc)
bndsc = bond_keys(xgrc)
atmsd = atoms(xgrd)
neighsd = atom_neighbor_keys(xgrd)
bndsd = bond_keys(xgrd)
tra = _substitution(atmsa, neighsa, bndsa, atmsb, xgr1, xgr2)
# tra = _substitution(
# atmsa, neighsa, bndsa, atmsb, neighsb, xgr1, xgr2)
idxs = [[0, 1], [0, 1]]
if not tra:
tra = _substitution(atmsb, neighsb, bndsb, atmsa, xgr1, xgr2)
# atmsb, neighsb, bndsb, atmsa, neighsa, xgr1, xgr2)
idxs = [[0, 1], [1, 0]]
if not tra:
tra = _substitution(atmsc, neighsc, bndsc, atmsd, xgr2, xgr1)
# atmsc, neighsc, bndsc, atmsd, neighsd, xgr2, xgr1)
idxs = [[1, 0], [0, 1]]
if not tra:
tra = _substitution(atmsd, neighsd, bndsd, atmsc, xgr2,
xgr1)
# atmsd, neighsd, bndsd, atmsc, neighsc, xgr2, xgr1)
idxs = [[1, 0], [1, 0]]
if not tra:
idxs = None
# return not substitution for radical + unsaturated reactions
unsat_atm_keys = _unsaturated_atom_keys(xgra)
# print('unsat test:', tra[0][0], unsat_atm_keys)
tra_list = list(tra[0])
for key in unsat_atm_keys:
if key in tra_list[0]:
pass
# tra = None
# commented out the tra = None and added pass to run CO + HO2
return tra, idxs
def union(gra1, gra2, check=True):
""" a union of two graphs
"""
if check:
assert not atom_keys(gra1) & atom_keys(gra2)
atm_dct = {}
atm_dct.update(atoms(gra1))
atm_dct.update(atoms(gra2))
bnd_dct = {}
bnd_dct.update(bonds(gra1))
bnd_dct.update(bonds(gra2))
return _create.graph.from_atoms_and_bonds(atm_dct, bnd_dct)
def atom_count(gra, dummy=False, with_implicit=True):
""" count the number of atoms in this molecule
by default, this includes implicit hydrogens and excludes dummy atoms
"""
if not dummy:
gra = without_dummy_atoms(gra)
natms = len(atoms(gra))
if with_implicit:
atm_imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(gra)
natms += sum(atm_imp_hyd_vlc_dct.values())
return natms
def radical_group_dct(gra):
""" return a dictionary of lists of groups attached each radical
"""
gra = without_fractional_bonds(gra)
groups = {}
rads = list(sing_res_dom_radical_atom_keys(gra))
atms = atoms(gra)
for rad in rads:
key = atms[rad][0]
if key in groups:
groups[atms[rad][0]] += atom_groups(gra, rad)
else:
groups[atms[rad][0]] = atom_groups(gra, rad)
return groups
def frozen(gra):
""" hashable, sortable, immutable container of graph data
"""
atm_keys = sorted(atom_keys(gra))
bnd_keys = sorted(bond_keys(gra), key=sorted)
# make it sortable by replacing Nones with -infinity
atm_vals = numpy.array(dict_.values_by_key(atoms(gra), atm_keys),
dtype=numpy.object)
bnd_vals = numpy.array(dict_.values_by_key(bonds(gra), bnd_keys),
dtype=numpy.object)
atm_vals[numpy.equal(atm_vals, None)] = -numpy.inf
bnd_vals[numpy.equal(bnd_vals, None)] = -numpy.inf
frz_atms = tuple(zip(atm_keys, map(tuple, atm_vals)))
frz_bnds = tuple(zip(bnd_keys, map(tuple, bnd_vals)))
return (frz_atms, frz_bnds)
def elimination(xgr1, xgr2):
"""identifies elimination reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
tras = []
if len(xgrs1) == 1 and len(xgrs2) == 2:
atms = atoms(xgr1)
neighs = atom_neighbor_keys(xgr1)
bnds = bond_keys(xgr1)
radicals = _resonance_dominant_radical_atom_keys(xgr1)
lonepairs = atom_lone_pair_counts(xgr1)
for atmi in atms:
i_neighs = neighs[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgra, xgrb = new_xgrs
atmsa = atoms(xgra)
if atmi not in atmsa.keys():
xgrb, xgra = xgra, xgrb
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
atmsb = atoms(xgrb)
neighs_i = neighsa[atmi]
for atmk in atmsb:
if atmk in radicals:
for atml in neighs_i:
neighs_l = neighsa[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
for atmi in atms:
i_neighs = neighs[atmi]
print('atmi test:', atmi)
print('i_neighs test:', i_neighs)
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgra, xgrb = new_xgrs
atmsa = atoms(xgra)
if atmi not in atmsa.keys():
xgrb, xgra = xgra, xgrb
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
atmsb = atoms(xgrb)
neighs_i = neighsa[atmi]
print('len atmsb test:', len(atmsb))
for atmk in atmsb:
if lonepairs[atmk] > 0 or len(atmsb) == 1:
# if lonepairs[atmk] > 0:
for atml in neighs_i:
neighs_l = neighsa[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
if len(tras) < 1:
tras = None
return tras
